Alignments for a candidate for edd in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas putida KT2440

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate PP_1010 PP_1010 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Putida:PP_1010
          Length = 608

 Score = 1056 bits (2732), Expect = 0.0
 Identities = 528/608 (86%), Positives = 566/608 (93%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPR+LEVT+RLV RSRATRE YL LIRGAAS+GP R  LQCANFAHGVAGCGSEDK +L
Sbjct: 1   MHPRILEVTQRLVERSRATRERYLQLIRGAASEGPMRASLQCANFAHGVAGCGSEDKQTL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R+MNAANVAIVS+YNDMLSAHQPY HFPEQIK+ALRE+GSVGQFAGG PAMCDGVTQGE 
Sbjct: 61  RLMNAANVAIVSAYNDMLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMEL++ SREVIA+STAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELAIASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNK+KADVRQRYAEGKA+REELLESEM SYHSPGTCTFYGTANTNQL+MEVMGLH
Sbjct: 181 MVSGISNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGTANTNQLVMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNPYTPLRDALT EAAQQVTR+TK SG+F P+GEIVDE++LVNSIVALHATGGS
Sbjct: 241 LPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLH+PAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL
Sbjct: 301 TNHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGLLHEDVNTVAG GL RYTQEPFLDNGKLVWR+GP  SLDE+ILRPV+R FS EGGL
Sbjct: 361 LDAGLLHEDVNTVAGHGLRRYTQEPFLDNGKLVWREGPQHSLDESILRPVSRPFSAEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA +HQ+VEAPA VFQDQQ LADAFKAGELE+DFVAV+RFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQVVEAPARVFQDQQSLADAFKAGELERDFVAVVRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
            NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGKIPAAIHV PEA  GG LARVRD
Sbjct: 481 CNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVCPEAYDGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDI+RVDGV+GTL + V A+E A+RE      GN++G GRELFGFMRMAFS AEQGASAF
Sbjct: 541 GDIVRVDGVEGTLRIMVSAEELASRELPPAPQGNDLGCGRELFGFMRMAFSPAEQGASAF 600

Query: 601 TSALENLK 608
           TSALE+LK
Sbjct: 601 TSALEHLK 608


Lambda     K      H
   0.318    0.134    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1306
Number of extensions: 55
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 608
Length of database: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate PP_1010 PP_1010 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01196.hmm
# target sequence database:        /tmp/gapView.5621.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01196  [M=601]
Accession:   TIGR01196
Description: edd: phosphogluconate dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1049.0   0.1          0 1048.8   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_1010  PP_1010 phosphogluconate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1010  PP_1010 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1048.8   0.1         0         0       1     601 []       2     601 ..       2     601 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1048.8 bits;  conditional E-value: 0
                           TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                         h+r++e+t+r++ers++tre+yl+ ir a+++g++r++l c+n+ahgva +  ++k++l+ ++ +n+ai++aynd
  lcl|FitnessBrowser__Putida:PP_1010   2 HPRILEVTQRLVERSRATRERYLQLIRGAASEGPMRASLQCANFAHGVAGCGSEDKQTLRLMNAANVAIVSAYND 76 
                                         79************************************************************************* PP

                           TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150
                                         mlsahqp+ ++p++ik+al+e ++v+q agGvpamcdGvtqGe+Gmel+++sr+via+sta++lshnmfd+al+l
  lcl|FitnessBrowser__Putida:PP_1010  77 MLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEPGMELAIASREVIAMSTAVALSHNMFDAALML 151
                                         *************************************************************************** PP

                           TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225
                                         G+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtctfyGt
  lcl|FitnessBrowser__Putida:PP_1010 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGT 226
                                         *************************************************************************** PP

                           TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300
                                         an+nq+++e+mGlhlpgasfvnp+tplrdalt+eaa++++r+t  +g+++pl+e++dek++vn++v+l+atGGst
  lcl|FitnessBrowser__Putida:PP_1010 227 ANTNQLVMEVMGLHLPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGST 301
                                         *************************************************************************** PP

                           TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375
                                         nhtlh+ aia+aaGi+l+w+d+ +ls++vp+l +vypnGkad+nhf+aaGG++flirell++Gllhedv+tvag+
  lcl|FitnessBrowser__Putida:PP_1010 302 NHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLDAGLLHEDVNTVAGH 376
                                         *************************************************************************** PP

                           TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450
                                         Glrryt+epfl++gkl++re++++slde+ilr+v++pfsaeGGl++++GnlGr+v+kvsav++e++v+eapa+vf
  lcl|FitnessBrowser__Putida:PP_1010 377 GLRRYTQEPFLDNGKLVWREGPQHSLDESILRPVSRPFSAEGGLRVMEGNLGRGVMKVSAVAPEHQVVEAPARVF 451
                                         *************************************************************************** PP

                           TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525
                                         +dq++l++afkagelerd+vavvrfqGp++nGmpelhklt++lGvlqdrg+kvalvtdGr+sGasGk+paaihv+
  lcl|FitnessBrowser__Putida:PP_1010 452 QDQQSLADAFKAGELERDFVAVVRFQGPRCNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVC 526
                                         *************************************************************************** PP

                           TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                         pea++gG+la++rdGd++r+d+v+g l+++v   el++re   ++++ n+lG+Grelf ++r + s ae+Gas++
  lcl|FitnessBrowser__Putida:PP_1010 527 PEAYDGGPLARVRDGDIVRVDGVEGTLRIMVSAEELASRE-LPPAPQGNDLGCGRELFGFMRMAFSPAEQGASAF 600
                                         ***************************************9.6899***************************998 PP

                           TIGR01196 601 t 601
                                         t
  lcl|FitnessBrowser__Putida:PP_1010 601 T 601
                                         6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.24
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources